Multiple sequence alignment - TraesCS2B01G181700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G181700 chr2B 100.000 5488 0 0 1 5488 156598474 156592987 0.000000e+00 10135.0
1 TraesCS2B01G181700 chr2B 85.496 131 16 2 617 746 72715002 72714874 3.450000e-27 134.0
2 TraesCS2B01G181700 chr2B 96.000 50 0 2 2947 2995 642790979 642791027 4.560000e-11 80.5
3 TraesCS2B01G181700 chr2A 94.548 4072 141 34 754 4781 103105505 103101471 0.000000e+00 6215.0
4 TraesCS2B01G181700 chr2A 91.650 491 31 8 5003 5488 103101292 103100807 0.000000e+00 671.0
5 TraesCS2B01G181700 chr2A 91.837 98 2 1 5390 5487 251390719 251390810 1.240000e-26 132.0
6 TraesCS2B01G181700 chr2A 93.651 63 3 1 3059 3120 533899609 533899671 5.850000e-15 93.5
7 TraesCS2B01G181700 chr2D 92.380 1168 55 15 754 1888 106632660 106631494 0.000000e+00 1633.0
8 TraesCS2B01G181700 chr2D 92.358 772 29 14 4724 5488 106628661 106627913 0.000000e+00 1072.0
9 TraesCS2B01G181700 chr2D 91.938 645 43 4 3118 3756 106630475 106629834 0.000000e+00 894.0
10 TraesCS2B01G181700 chr2D 90.844 557 30 9 3755 4295 106629758 106629207 0.000000e+00 726.0
11 TraesCS2B01G181700 chr2D 90.101 495 41 6 1914 2405 106631497 106631008 2.160000e-178 636.0
12 TraesCS2B01G181700 chr2D 93.766 385 21 3 4347 4731 106629205 106628824 4.770000e-160 575.0
13 TraesCS2B01G181700 chr2D 85.851 417 42 8 2484 2888 106631010 106630599 1.410000e-115 427.0
14 TraesCS2B01G181700 chr2D 89.340 197 8 6 1471 1655 581246949 581246754 9.190000e-58 235.0
15 TraesCS2B01G181700 chr2D 91.473 129 10 1 621 748 19392075 19391947 5.650000e-40 176.0
16 TraesCS2B01G181700 chr2D 85.890 163 23 0 2957 3119 618204765 618204927 2.030000e-39 174.0
17 TraesCS2B01G181700 chr2D 89.109 101 3 5 5388 5488 407438898 407438990 9.660000e-23 119.0
18 TraesCS2B01G181700 chr2D 95.946 74 1 2 5388 5461 622711270 622711341 9.660000e-23 119.0
19 TraesCS2B01G181700 chr4B 88.197 610 57 9 2 600 290914491 290913886 0.000000e+00 713.0
20 TraesCS2B01G181700 chr5D 84.539 608 59 17 3 601 124388371 124387790 2.220000e-158 569.0
21 TraesCS2B01G181700 chr5D 91.111 45 4 0 288 332 214364629 214364673 1.650000e-05 62.1
22 TraesCS2B01G181700 chr1B 81.536 612 93 14 4 601 442155602 442156207 2.300000e-133 486.0
23 TraesCS2B01G181700 chr1B 83.333 132 21 1 2957 3088 9984784 9984914 2.690000e-23 121.0
24 TraesCS2B01G181700 chr6B 89.600 125 12 1 626 749 125632984 125632860 2.050000e-34 158.0
25 TraesCS2B01G181700 chr6B 92.424 66 5 0 3052 3117 607123784 607123719 1.630000e-15 95.3
26 TraesCS2B01G181700 chr6A 87.591 137 16 1 615 750 163199410 163199274 2.050000e-34 158.0
27 TraesCS2B01G181700 chr6A 92.000 100 2 1 5388 5487 595732651 595732744 9.590000e-28 135.0
28 TraesCS2B01G181700 chr1A 82.558 172 29 1 2944 3114 41515654 41515825 3.420000e-32 150.0
29 TraesCS2B01G181700 chr7A 82.927 164 28 0 2954 3117 641636573 641636736 1.230000e-31 148.0
30 TraesCS2B01G181700 chr7B 82.317 164 29 0 2954 3117 695899354 695899517 5.730000e-30 143.0
31 TraesCS2B01G181700 chr7B 84.956 113 16 1 2936 3048 716284081 716283970 4.490000e-21 113.0
32 TraesCS2B01G181700 chr4D 93.069 101 1 1 5388 5488 46139925 46139831 5.730000e-30 143.0
33 TraesCS2B01G181700 chr4D 90.816 98 1 5 5391 5488 328719234 328719145 2.080000e-24 124.0
34 TraesCS2B01G181700 chr5B 90.291 103 8 2 649 749 505792718 505792616 3.450000e-27 134.0
35 TraesCS2B01G181700 chr5B 91.089 101 3 1 5388 5488 236414536 236414630 1.240000e-26 132.0
36 TraesCS2B01G181700 chr1D 81.707 164 20 1 2954 3117 22436082 22436235 1.600000e-25 128.0
37 TraesCS2B01G181700 chr4A 81.325 166 17 5 2954 3117 740462112 740461959 7.470000e-24 122.0
38 TraesCS2B01G181700 chr7D 81.679 131 13 3 2987 3117 2351229 2351348 1.260000e-16 99.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G181700 chr2B 156592987 156598474 5487 True 10135.000000 10135 100.000 1 5488 1 chr2B.!!$R2 5487
1 TraesCS2B01G181700 chr2A 103100807 103105505 4698 True 3443.000000 6215 93.099 754 5488 2 chr2A.!!$R1 4734
2 TraesCS2B01G181700 chr2D 106627913 106632660 4747 True 851.857143 1633 91.034 754 5488 7 chr2D.!!$R3 4734
3 TraesCS2B01G181700 chr4B 290913886 290914491 605 True 713.000000 713 88.197 2 600 1 chr4B.!!$R1 598
4 TraesCS2B01G181700 chr5D 124387790 124388371 581 True 569.000000 569 84.539 3 601 1 chr5D.!!$R1 598
5 TraesCS2B01G181700 chr1B 442155602 442156207 605 False 486.000000 486 81.536 4 601 1 chr1B.!!$F2 597

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
750 790 0.037160 GGTTTCCGAACAGGGCCTAA 59.963 55.000 5.28 0.00 41.52 2.69 F
1467 1518 0.668401 GTTGCTTGACATGGCTTGCC 60.668 55.000 12.51 4.43 0.00 4.52 F
1486 1537 1.303643 GTCTGGCCTTCCTTGTGGG 60.304 63.158 3.32 0.00 0.00 4.61 F
1488 1539 1.604593 CTGGCCTTCCTTGTGGGTG 60.605 63.158 3.32 0.00 36.25 4.61 F
1570 1629 1.884579 AGGTGCTTGACAGATGCTTTG 59.115 47.619 0.00 0.00 0.00 2.77 F
3081 3189 3.712091 ATAGCGTTTAGAAGAGGTCCG 57.288 47.619 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 2022 0.178992 ACTGGCACAAGGCTAAGCAA 60.179 50.000 7.82 0.00 44.01 3.91 R
2986 3094 0.389948 GACCAGTGTCCCTTAGCACG 60.390 60.000 0.00 0.00 40.26 5.34 R
3081 3189 0.610687 AGGATATGCCTCTTAGCGGC 59.389 55.000 6.25 6.25 46.97 6.53 R
3352 3460 1.408969 TGTTTTCCAGCCCCTGAAAC 58.591 50.000 0.00 0.00 32.46 2.78 R
3824 4015 7.285401 GGATAAAGGCTTCTGTCAAATAATGGA 59.715 37.037 0.00 0.00 0.00 3.41 R
5215 5671 1.334869 CAACGGCTGGATATTTGCCTC 59.665 52.381 0.00 0.00 44.09 4.70 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.348696 TCATCTGGCTTGCAGTTCAGA 59.651 47.619 14.35 14.35 40.04 3.27
54 55 0.968901 TAGATGTTGGACGGCGGACT 60.969 55.000 13.24 0.00 0.00 3.85
56 57 2.501223 GATGTTGGACGGCGGACTGA 62.501 60.000 13.24 0.00 0.00 3.41
82 83 1.431488 CGTCATGGCCTTGATCACCG 61.431 60.000 22.94 17.36 0.00 4.94
107 108 4.594854 TGCCCTTTCTGCGCCCAA 62.595 61.111 4.18 0.00 0.00 4.12
122 123 0.391661 CCCAACACGAGGAGACCATG 60.392 60.000 0.00 0.00 0.00 3.66
156 157 1.621317 TGAACTACGTCATGGCAAGGA 59.379 47.619 0.00 0.00 0.00 3.36
177 200 4.399934 GGAAGGTTTGGACTGTTGTTTGTA 59.600 41.667 0.00 0.00 0.00 2.41
178 201 5.068591 GGAAGGTTTGGACTGTTGTTTGTAT 59.931 40.000 0.00 0.00 0.00 2.29
185 208 4.037446 TGGACTGTTGTTTGTATGGCTTTC 59.963 41.667 0.00 0.00 0.00 2.62
198 221 1.285950 GCTTTCAACAAGCCGGGAC 59.714 57.895 2.18 0.00 37.30 4.46
228 251 2.425312 ACAAGCGAAACAACATTGGTGA 59.575 40.909 9.09 0.00 0.00 4.02
245 268 0.531974 TGAAGTGGTGTGCGGAGAAC 60.532 55.000 0.00 0.00 0.00 3.01
270 293 1.884579 ACACAAGCCAGAGCATGAAAG 59.115 47.619 0.00 0.00 40.14 2.62
285 308 0.938008 GAAAGGAATGCGGACGATCC 59.062 55.000 0.00 0.00 0.00 3.36
371 395 2.028112 TCCTTGCGAGTCTTGCTACAAT 60.028 45.455 13.35 0.00 0.00 2.71
377 401 4.119862 GCGAGTCTTGCTACAATCCATTA 58.880 43.478 4.68 0.00 0.00 1.90
387 411 5.191722 TGCTACAATCCATTAAGAGGGAAGT 59.808 40.000 0.00 0.00 39.54 3.01
424 448 3.325135 CAGCGGGACTTATAAAGGGAGAT 59.675 47.826 0.00 0.00 0.00 2.75
452 478 2.092914 GCTCTTTTTAGGGCTGGCTAGA 60.093 50.000 0.00 0.00 0.00 2.43
464 490 2.533916 CTGGCTAGATGGGAGAGCATA 58.466 52.381 0.00 0.00 37.98 3.14
479 505 6.826741 GGGAGAGCATAAGAGAGTAGTATAGG 59.173 46.154 0.00 0.00 0.00 2.57
513 552 3.886505 TGGAGTTGGGTTTCATGTAACAC 59.113 43.478 15.91 13.25 31.98 3.32
525 564 5.284861 TCATGTAACACTGTGTAACACCT 57.715 39.130 14.69 0.00 45.67 4.00
538 577 2.844394 ACACCTAACGTGAAGGGGT 58.156 52.632 17.28 17.28 46.23 4.95
601 641 6.417635 CACACTTGTGCGTATTTGAGAAAAAT 59.582 34.615 0.10 0.00 39.39 1.82
602 642 7.589587 CACACTTGTGCGTATTTGAGAAAAATA 59.410 33.333 0.10 0.00 39.39 1.40
603 643 7.803189 ACACTTGTGCGTATTTGAGAAAAATAG 59.197 33.333 0.10 0.00 0.00 1.73
604 644 8.015087 CACTTGTGCGTATTTGAGAAAAATAGA 58.985 33.333 0.00 0.00 0.00 1.98
605 645 8.730680 ACTTGTGCGTATTTGAGAAAAATAGAT 58.269 29.630 0.00 0.00 0.00 1.98
606 646 9.214953 CTTGTGCGTATTTGAGAAAAATAGATC 57.785 33.333 0.00 0.00 0.00 2.75
607 647 7.398746 TGTGCGTATTTGAGAAAAATAGATCG 58.601 34.615 0.00 0.00 0.00 3.69
608 648 7.276878 TGTGCGTATTTGAGAAAAATAGATCGA 59.723 33.333 0.00 0.00 0.00 3.59
609 649 8.276325 GTGCGTATTTGAGAAAAATAGATCGAT 58.724 33.333 0.00 0.00 0.00 3.59
610 650 9.471084 TGCGTATTTGAGAAAAATAGATCGATA 57.529 29.630 0.00 0.00 0.00 2.92
611 651 9.944941 GCGTATTTGAGAAAAATAGATCGATAG 57.055 33.333 0.00 0.00 0.00 2.08
623 663 9.832445 AAAATAGATCGATAGTTTTCTAAGGCA 57.168 29.630 0.00 0.00 35.90 4.75
626 666 7.721286 AGATCGATAGTTTTCTAAGGCATTG 57.279 36.000 0.00 0.00 35.90 2.82
627 667 7.275920 AGATCGATAGTTTTCTAAGGCATTGT 58.724 34.615 0.00 0.00 35.90 2.71
628 668 7.770897 AGATCGATAGTTTTCTAAGGCATTGTT 59.229 33.333 0.00 0.00 35.90 2.83
629 669 7.303634 TCGATAGTTTTCTAAGGCATTGTTC 57.696 36.000 0.00 0.00 35.90 3.18
630 670 6.876789 TCGATAGTTTTCTAAGGCATTGTTCA 59.123 34.615 0.00 0.00 35.90 3.18
631 671 7.064609 TCGATAGTTTTCTAAGGCATTGTTCAG 59.935 37.037 0.00 0.00 35.90 3.02
632 672 7.064609 CGATAGTTTTCTAAGGCATTGTTCAGA 59.935 37.037 0.00 0.00 35.90 3.27
633 673 6.959639 AGTTTTCTAAGGCATTGTTCAGAA 57.040 33.333 0.00 0.00 0.00 3.02
634 674 7.530426 AGTTTTCTAAGGCATTGTTCAGAAT 57.470 32.000 0.00 0.00 0.00 2.40
635 675 7.597386 AGTTTTCTAAGGCATTGTTCAGAATC 58.403 34.615 0.00 0.00 0.00 2.52
636 676 5.801350 TTCTAAGGCATTGTTCAGAATCG 57.199 39.130 0.00 0.00 0.00 3.34
637 677 2.927553 AAGGCATTGTTCAGAATCGC 57.072 45.000 0.00 0.00 0.00 4.58
638 678 2.119801 AGGCATTGTTCAGAATCGCT 57.880 45.000 0.00 0.00 0.00 4.93
639 679 2.012673 AGGCATTGTTCAGAATCGCTC 58.987 47.619 0.00 0.00 0.00 5.03
640 680 1.064654 GGCATTGTTCAGAATCGCTCC 59.935 52.381 0.00 0.00 0.00 4.70
641 681 1.739466 GCATTGTTCAGAATCGCTCCA 59.261 47.619 0.00 0.00 0.00 3.86
642 682 2.476854 GCATTGTTCAGAATCGCTCCAC 60.477 50.000 0.00 0.00 0.00 4.02
643 683 2.839486 TTGTTCAGAATCGCTCCACT 57.161 45.000 0.00 0.00 0.00 4.00
644 684 2.370281 TGTTCAGAATCGCTCCACTC 57.630 50.000 0.00 0.00 0.00 3.51
645 685 1.066858 TGTTCAGAATCGCTCCACTCC 60.067 52.381 0.00 0.00 0.00 3.85
646 686 0.173481 TTCAGAATCGCTCCACTCCG 59.827 55.000 0.00 0.00 0.00 4.63
647 687 1.880340 CAGAATCGCTCCACTCCGC 60.880 63.158 0.00 0.00 0.00 5.54
648 688 2.184322 GAATCGCTCCACTCCGCA 59.816 61.111 0.00 0.00 0.00 5.69
649 689 1.447838 GAATCGCTCCACTCCGCAA 60.448 57.895 0.00 0.00 0.00 4.85
650 690 1.696832 GAATCGCTCCACTCCGCAAC 61.697 60.000 0.00 0.00 0.00 4.17
651 691 2.172483 AATCGCTCCACTCCGCAACT 62.172 55.000 0.00 0.00 0.00 3.16
652 692 2.564553 ATCGCTCCACTCCGCAACTC 62.565 60.000 0.00 0.00 0.00 3.01
653 693 2.343758 GCTCCACTCCGCAACTCA 59.656 61.111 0.00 0.00 0.00 3.41
654 694 1.739562 GCTCCACTCCGCAACTCAG 60.740 63.158 0.00 0.00 0.00 3.35
655 695 1.739562 CTCCACTCCGCAACTCAGC 60.740 63.158 0.00 0.00 0.00 4.26
656 696 2.164865 CTCCACTCCGCAACTCAGCT 62.165 60.000 0.00 0.00 0.00 4.24
657 697 1.739562 CCACTCCGCAACTCAGCTC 60.740 63.158 0.00 0.00 0.00 4.09
658 698 1.739562 CACTCCGCAACTCAGCTCC 60.740 63.158 0.00 0.00 0.00 4.70
659 699 1.910772 ACTCCGCAACTCAGCTCCT 60.911 57.895 0.00 0.00 0.00 3.69
660 700 1.447489 CTCCGCAACTCAGCTCCTG 60.447 63.158 0.00 0.00 0.00 3.86
661 701 2.435586 CCGCAACTCAGCTCCTGG 60.436 66.667 0.00 0.00 31.51 4.45
662 702 2.659016 CGCAACTCAGCTCCTGGA 59.341 61.111 0.00 0.00 31.51 3.86
663 703 1.447489 CGCAACTCAGCTCCTGGAG 60.447 63.158 19.55 19.55 31.51 3.86
688 728 2.972625 CGGAGCTGTAGTTGGAAATCA 58.027 47.619 0.00 0.00 0.00 2.57
689 729 2.932614 CGGAGCTGTAGTTGGAAATCAG 59.067 50.000 0.00 0.00 0.00 2.90
690 730 3.274288 GGAGCTGTAGTTGGAAATCAGG 58.726 50.000 0.00 0.00 0.00 3.86
691 731 3.274288 GAGCTGTAGTTGGAAATCAGGG 58.726 50.000 0.00 0.00 0.00 4.45
692 732 2.912956 AGCTGTAGTTGGAAATCAGGGA 59.087 45.455 0.00 0.00 0.00 4.20
693 733 3.330701 AGCTGTAGTTGGAAATCAGGGAA 59.669 43.478 0.00 0.00 0.00 3.97
694 734 3.440522 GCTGTAGTTGGAAATCAGGGAAC 59.559 47.826 0.00 0.00 0.00 3.62
695 735 4.807643 GCTGTAGTTGGAAATCAGGGAACT 60.808 45.833 0.00 0.00 46.44 3.01
707 747 1.826385 AGGGAACTGCATTTTCCTCG 58.174 50.000 20.99 0.00 42.10 4.63
708 748 0.171231 GGGAACTGCATTTTCCTCGC 59.829 55.000 20.99 6.68 42.10 5.03
709 749 1.168714 GGAACTGCATTTTCCTCGCT 58.831 50.000 16.60 0.00 39.68 4.93
710 750 1.541588 GGAACTGCATTTTCCTCGCTT 59.458 47.619 16.60 0.00 39.68 4.68
711 751 2.414691 GGAACTGCATTTTCCTCGCTTC 60.415 50.000 16.60 0.00 39.68 3.86
712 752 1.168714 ACTGCATTTTCCTCGCTTCC 58.831 50.000 0.00 0.00 0.00 3.46
713 753 0.097674 CTGCATTTTCCTCGCTTCCG 59.902 55.000 0.00 0.00 0.00 4.30
714 754 0.321210 TGCATTTTCCTCGCTTCCGA 60.321 50.000 0.00 0.00 42.01 4.55
723 763 1.816537 TCGCTTCCGAGATTCCTGG 59.183 57.895 0.00 0.00 38.82 4.45
724 764 0.683179 TCGCTTCCGAGATTCCTGGA 60.683 55.000 0.00 0.00 38.82 3.86
725 765 0.249238 CGCTTCCGAGATTCCTGGAG 60.249 60.000 0.00 0.00 36.29 3.86
726 766 0.531753 GCTTCCGAGATTCCTGGAGC 60.532 60.000 0.00 0.00 32.39 4.70
727 767 0.249238 CTTCCGAGATTCCTGGAGCG 60.249 60.000 0.00 0.16 32.39 5.03
728 768 1.676678 TTCCGAGATTCCTGGAGCGG 61.677 60.000 17.62 17.62 40.06 5.52
729 769 2.427245 CCGAGATTCCTGGAGCGGT 61.427 63.158 16.28 0.00 34.45 5.68
730 770 1.227089 CGAGATTCCTGGAGCGGTG 60.227 63.158 0.00 0.00 0.00 4.94
731 771 1.144936 GAGATTCCTGGAGCGGTGG 59.855 63.158 0.00 0.00 0.00 4.61
732 772 2.190578 GATTCCTGGAGCGGTGGG 59.809 66.667 0.00 0.00 0.00 4.61
733 773 2.610859 ATTCCTGGAGCGGTGGGT 60.611 61.111 0.00 0.00 0.00 4.51
734 774 2.198304 GATTCCTGGAGCGGTGGGTT 62.198 60.000 0.00 0.00 0.00 4.11
735 775 1.789576 ATTCCTGGAGCGGTGGGTTT 61.790 55.000 0.00 0.00 0.00 3.27
736 776 2.359975 CCTGGAGCGGTGGGTTTC 60.360 66.667 0.00 0.00 0.00 2.78
737 777 2.359975 CTGGAGCGGTGGGTTTCC 60.360 66.667 0.00 0.00 0.00 3.13
744 784 4.074647 GGTGGGTTTCCGAACAGG 57.925 61.111 0.00 0.00 37.51 4.00
745 785 1.602605 GGTGGGTTTCCGAACAGGG 60.603 63.158 0.00 0.00 41.52 4.45
746 786 2.114411 TGGGTTTCCGAACAGGGC 59.886 61.111 0.00 0.00 41.52 5.19
747 787 2.675423 GGGTTTCCGAACAGGGCC 60.675 66.667 0.00 0.00 41.52 5.80
748 788 2.434774 GGTTTCCGAACAGGGCCT 59.565 61.111 0.00 0.00 41.52 5.19
749 789 1.681076 GGTTTCCGAACAGGGCCTA 59.319 57.895 5.28 0.00 41.52 3.93
750 790 0.037160 GGTTTCCGAACAGGGCCTAA 59.963 55.000 5.28 0.00 41.52 2.69
751 791 1.546099 GGTTTCCGAACAGGGCCTAAA 60.546 52.381 5.28 0.00 41.52 1.85
752 792 1.538512 GTTTCCGAACAGGGCCTAAAC 59.461 52.381 5.28 8.77 41.52 2.01
857 899 3.745803 GTCGAACCGGAGCCGAGT 61.746 66.667 9.46 3.89 42.83 4.18
909 951 2.060980 GCGACCTCATCCCTCCACT 61.061 63.158 0.00 0.00 0.00 4.00
988 1038 2.515057 ACGCAAACCCGCAGACAA 60.515 55.556 0.00 0.00 0.00 3.18
1163 1213 2.437716 CCGCCCCGCATGTAACTT 60.438 61.111 0.00 0.00 0.00 2.66
1166 1216 1.077716 GCCCCGCATGTAACTTCCT 60.078 57.895 0.00 0.00 0.00 3.36
1268 1318 2.935740 GCCTGTCCCTTTGCTTGGC 61.936 63.158 0.00 0.00 0.00 4.52
1314 1364 1.134075 CTGAACAGTGAGCGCATGC 59.866 57.895 11.47 7.91 43.24 4.06
1336 1386 2.874086 CTGATGCAACGCTGATATCCAA 59.126 45.455 0.00 0.00 0.00 3.53
1390 1441 2.573462 ACTGTGGAATGCCTGTATGACT 59.427 45.455 0.00 0.00 34.31 3.41
1467 1518 0.668401 GTTGCTTGACATGGCTTGCC 60.668 55.000 12.51 4.43 0.00 4.52
1469 1520 2.629656 GCTTGACATGGCTTGCCGT 61.630 57.895 0.00 3.61 0.00 5.68
1485 1536 1.672356 CGTCTGGCCTTCCTTGTGG 60.672 63.158 3.32 0.00 0.00 4.17
1486 1537 1.303643 GTCTGGCCTTCCTTGTGGG 60.304 63.158 3.32 0.00 0.00 4.61
1487 1538 1.774217 TCTGGCCTTCCTTGTGGGT 60.774 57.895 3.32 0.00 36.25 4.51
1488 1539 1.604593 CTGGCCTTCCTTGTGGGTG 60.605 63.158 3.32 0.00 36.25 4.61
1570 1629 1.884579 AGGTGCTTGACAGATGCTTTG 59.115 47.619 0.00 0.00 0.00 2.77
1790 1869 5.280317 GGGGAATACTGAAGGTGTAAGACAA 60.280 44.000 0.00 0.00 0.00 3.18
1943 2022 6.817765 AAGTGTTGAACATGACGGATTTAT 57.182 33.333 0.00 0.00 0.00 1.40
2085 2164 5.048083 TCAGGGCTGAATACAATTTTGTGTC 60.048 40.000 6.21 4.54 38.11 3.67
2427 2507 4.869297 TGGTTTTGATTGCAAGTGTGAAAG 59.131 37.500 4.94 0.00 35.04 2.62
2491 2571 9.280174 TCCGTTACTTCAGTTTTCTATTTCAAT 57.720 29.630 0.00 0.00 0.00 2.57
2711 2791 8.627208 TCCATTTATTTCCTATCATTCTGAGC 57.373 34.615 0.00 0.00 0.00 4.26
2798 2889 8.879342 TGACTAGCTAAATCTTTCTCAATAGC 57.121 34.615 0.00 0.00 36.80 2.97
2889 2997 8.942338 AGCTTTGTAGTCAATTCGATGTATTA 57.058 30.769 0.00 0.00 33.32 0.98
2956 3064 4.915704 GCATGGTTTTAAATAGCGTGCTA 58.084 39.130 23.99 3.73 46.84 3.49
2986 3094 5.507650 CGCTATAGTGTTTAGAAGAGGTCCC 60.508 48.000 5.07 0.00 0.00 4.46
3030 3138 8.731605 TCTAAACACATGAACACACACTTTAAA 58.268 29.630 0.00 0.00 0.00 1.52
3081 3189 3.712091 ATAGCGTTTAGAAGAGGTCCG 57.288 47.619 0.00 0.00 0.00 4.79
3235 3343 4.631377 TGCAGTGTGAGCTATACAACATTC 59.369 41.667 4.97 0.00 0.00 2.67
3283 3391 4.811024 TGCTGTTTAATTAGCTCTCATCGG 59.189 41.667 11.35 0.00 40.52 4.18
3352 3460 5.608676 AAGATTGATAGCATGCATCTTCG 57.391 39.130 21.98 0.00 0.00 3.79
4067 4276 1.066858 ACACATGTACTTCTGCCGAGG 60.067 52.381 0.00 0.00 0.00 4.63
4499 4708 1.741706 AGCGAATGACATTTGAGCAGG 59.258 47.619 18.05 0.00 0.00 4.85
4588 4798 2.821378 TGATGTTTGGAGGAGCACAATG 59.179 45.455 0.00 0.00 0.00 2.82
4631 4841 2.723124 TTTTGGCAAAAGAGCGGATC 57.277 45.000 20.81 0.00 34.64 3.36
4676 4891 0.449388 GTGTGCTAGCCATGTCTTGC 59.551 55.000 13.29 3.15 35.81 4.01
4701 4921 2.151202 TGCATTCGAAACCTTGAGACC 58.849 47.619 0.00 0.00 0.00 3.85
4723 4943 6.238648 ACCTTTCGGAACTTTGTATCATTCT 58.761 36.000 0.00 0.00 0.00 2.40
4799 5214 5.385198 TGGGACTGGGATGCTATAAAATTC 58.615 41.667 0.00 0.00 0.00 2.17
4814 5229 3.777465 AAATTCTGTGCTGCTGCTATG 57.223 42.857 17.00 6.55 40.48 2.23
4815 5230 2.414994 ATTCTGTGCTGCTGCTATGT 57.585 45.000 17.00 0.00 40.48 2.29
4816 5231 3.548745 ATTCTGTGCTGCTGCTATGTA 57.451 42.857 17.00 0.39 40.48 2.29
4884 5299 9.093970 GTTTTTACCACTTTCAACAAGCTAATT 57.906 29.630 0.00 0.00 0.00 1.40
4889 5304 5.241506 CCACTTTCAACAAGCTAATTCCTCA 59.758 40.000 0.00 0.00 0.00 3.86
4893 5308 8.257306 ACTTTCAACAAGCTAATTCCTCAAAAA 58.743 29.630 0.00 0.00 0.00 1.94
4972 5390 0.588252 CCACTTCACTTCCAGTTGCG 59.412 55.000 0.00 0.00 0.00 4.85
4984 5402 0.451783 CAGTTGCGGTGGGCTTTATC 59.548 55.000 0.00 0.00 44.05 1.75
5118 5573 4.615588 TCCCATCCAATTCCAACAAAAC 57.384 40.909 0.00 0.00 0.00 2.43
5166 5622 3.067091 CTGGCCTCTCACACTGCT 58.933 61.111 3.32 0.00 0.00 4.24
5192 5648 1.307343 CCACACCCCCTCTCATCCT 60.307 63.158 0.00 0.00 0.00 3.24
5194 5650 1.418334 CACACCCCCTCTCATCCTAG 58.582 60.000 0.00 0.00 0.00 3.02
5213 5669 3.214696 AGCCCCAGAAAAATATCTCCG 57.785 47.619 0.00 0.00 0.00 4.63
5215 5671 1.873591 CCCCAGAAAAATATCTCCGCG 59.126 52.381 0.00 0.00 0.00 6.46
5216 5672 2.484770 CCCCAGAAAAATATCTCCGCGA 60.485 50.000 8.23 0.00 0.00 5.87
5217 5673 2.802816 CCCAGAAAAATATCTCCGCGAG 59.197 50.000 8.23 3.02 0.00 5.03
5267 5723 2.111878 CTGGCCGTCCATCCATCC 59.888 66.667 0.00 0.00 42.51 3.51
5268 5724 3.814615 CTGGCCGTCCATCCATCCG 62.815 68.421 0.00 0.00 42.51 4.18
5272 5728 3.550431 CGTCCATCCATCCGCCCT 61.550 66.667 0.00 0.00 0.00 5.19
5328 5784 1.377333 CTCACCCCTTTCCCTTCGC 60.377 63.158 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.208431 CCAGATGAAGAATCGACAGCC 58.792 52.381 0.00 0.00 40.54 4.85
16 17 0.761187 ACTCTGAACTGCAAGCCAGA 59.239 50.000 10.08 10.08 44.64 3.86
33 34 0.968901 TCCGCCGTCCAACATCTACT 60.969 55.000 0.00 0.00 0.00 2.57
82 83 3.050275 AGAAAGGGCAAGCGTCGC 61.050 61.111 9.80 9.80 0.00 5.19
107 108 1.990060 CCCCATGGTCTCCTCGTGT 60.990 63.158 11.73 0.00 0.00 4.49
142 143 0.110486 AACCTTCCTTGCCATGACGT 59.890 50.000 0.00 0.00 0.00 4.34
156 157 5.163457 CCATACAAACAACAGTCCAAACCTT 60.163 40.000 0.00 0.00 0.00 3.50
185 208 4.636435 ACCCGTCCCGGCTTGTTG 62.636 66.667 0.00 0.00 46.86 3.33
228 251 0.107410 TTGTTCTCCGCACACCACTT 60.107 50.000 0.00 0.00 0.00 3.16
245 268 1.159713 TGCTCTGGCTTGTGTCGTTG 61.160 55.000 0.00 0.00 39.59 4.10
270 293 1.301009 GGAGGATCGTCCGCATTCC 60.301 63.158 18.18 0.00 42.75 3.01
285 308 2.103941 GCTCCCATAAGACAAGGAGGAG 59.896 54.545 7.01 0.00 45.08 3.69
371 395 2.504175 CCCGAACTTCCCTCTTAATGGA 59.496 50.000 0.00 0.00 0.00 3.41
377 401 0.036875 CAAGCCCGAACTTCCCTCTT 59.963 55.000 0.00 0.00 0.00 2.85
387 411 2.034066 CTGCCTTCCAAGCCCGAA 59.966 61.111 0.00 0.00 0.00 4.30
424 448 2.108250 AGCCCTAAAAAGAGCTTCCACA 59.892 45.455 0.00 0.00 29.27 4.17
452 478 5.073437 ACTACTCTCTTATGCTCTCCCAT 57.927 43.478 0.00 0.00 0.00 4.00
464 490 8.532819 CCACAAAGAAACCTATACTACTCTCTT 58.467 37.037 0.00 0.00 0.00 2.85
479 505 2.100749 CCCAACTCCACCACAAAGAAAC 59.899 50.000 0.00 0.00 0.00 2.78
525 564 1.345415 GGTGAGAACCCCTTCACGTTA 59.655 52.381 0.00 0.00 34.24 3.18
582 622 7.276878 TCGATCTATTTTTCTCAAATACGCACA 59.723 33.333 0.00 0.00 0.00 4.57
601 641 8.421784 ACAATGCCTTAGAAAACTATCGATCTA 58.578 33.333 0.00 0.00 0.00 1.98
602 642 7.275920 ACAATGCCTTAGAAAACTATCGATCT 58.724 34.615 0.00 0.00 0.00 2.75
603 643 7.484035 ACAATGCCTTAGAAAACTATCGATC 57.516 36.000 0.00 0.00 0.00 3.69
604 644 7.552687 TGAACAATGCCTTAGAAAACTATCGAT 59.447 33.333 2.16 2.16 0.00 3.59
605 645 6.876789 TGAACAATGCCTTAGAAAACTATCGA 59.123 34.615 0.00 0.00 0.00 3.59
606 646 7.064609 TCTGAACAATGCCTTAGAAAACTATCG 59.935 37.037 0.00 0.00 0.00 2.92
607 647 8.268850 TCTGAACAATGCCTTAGAAAACTATC 57.731 34.615 0.00 0.00 0.00 2.08
608 648 8.635765 TTCTGAACAATGCCTTAGAAAACTAT 57.364 30.769 0.00 0.00 0.00 2.12
609 649 8.635765 ATTCTGAACAATGCCTTAGAAAACTA 57.364 30.769 0.00 0.00 0.00 2.24
610 650 6.959639 TTCTGAACAATGCCTTAGAAAACT 57.040 33.333 0.00 0.00 0.00 2.66
611 651 6.524586 CGATTCTGAACAATGCCTTAGAAAAC 59.475 38.462 0.00 0.00 0.00 2.43
612 652 6.611381 CGATTCTGAACAATGCCTTAGAAAA 58.389 36.000 0.00 0.00 0.00 2.29
613 653 5.391950 GCGATTCTGAACAATGCCTTAGAAA 60.392 40.000 0.00 0.00 0.00 2.52
614 654 4.094887 GCGATTCTGAACAATGCCTTAGAA 59.905 41.667 0.00 0.00 0.00 2.10
615 655 3.623060 GCGATTCTGAACAATGCCTTAGA 59.377 43.478 0.00 0.00 0.00 2.10
616 656 3.624861 AGCGATTCTGAACAATGCCTTAG 59.375 43.478 0.00 0.00 0.00 2.18
617 657 3.609853 AGCGATTCTGAACAATGCCTTA 58.390 40.909 0.00 0.00 0.00 2.69
618 658 2.421424 GAGCGATTCTGAACAATGCCTT 59.579 45.455 0.00 0.00 0.00 4.35
619 659 2.012673 GAGCGATTCTGAACAATGCCT 58.987 47.619 0.00 0.00 0.00 4.75
620 660 1.064654 GGAGCGATTCTGAACAATGCC 59.935 52.381 0.00 0.00 0.00 4.40
621 661 1.739466 TGGAGCGATTCTGAACAATGC 59.261 47.619 0.00 0.00 0.00 3.56
622 662 3.005554 AGTGGAGCGATTCTGAACAATG 58.994 45.455 0.00 0.00 0.00 2.82
623 663 3.265791 GAGTGGAGCGATTCTGAACAAT 58.734 45.455 0.00 0.00 0.00 2.71
624 664 2.612972 GGAGTGGAGCGATTCTGAACAA 60.613 50.000 0.00 0.00 0.00 2.83
625 665 1.066858 GGAGTGGAGCGATTCTGAACA 60.067 52.381 0.00 0.00 0.00 3.18
626 666 1.646189 GGAGTGGAGCGATTCTGAAC 58.354 55.000 0.00 0.00 0.00 3.18
627 667 0.173481 CGGAGTGGAGCGATTCTGAA 59.827 55.000 0.00 0.00 0.00 3.02
628 668 1.809869 CGGAGTGGAGCGATTCTGA 59.190 57.895 0.00 0.00 0.00 3.27
629 669 1.880340 GCGGAGTGGAGCGATTCTG 60.880 63.158 0.00 0.00 0.00 3.02
630 670 1.888436 TTGCGGAGTGGAGCGATTCT 61.888 55.000 0.00 0.00 35.87 2.40
631 671 1.447838 TTGCGGAGTGGAGCGATTC 60.448 57.895 0.00 0.00 35.87 2.52
632 672 1.741770 GTTGCGGAGTGGAGCGATT 60.742 57.895 0.00 0.00 35.87 3.34
633 673 2.125512 GTTGCGGAGTGGAGCGAT 60.126 61.111 0.00 0.00 35.87 4.58
634 674 3.282745 GAGTTGCGGAGTGGAGCGA 62.283 63.158 0.00 0.00 35.87 4.93
635 675 2.811317 GAGTTGCGGAGTGGAGCG 60.811 66.667 0.00 0.00 35.87 5.03
636 676 1.739562 CTGAGTTGCGGAGTGGAGC 60.740 63.158 0.00 0.00 0.00 4.70
637 677 1.739562 GCTGAGTTGCGGAGTGGAG 60.740 63.158 0.00 0.00 0.00 3.86
638 678 2.159819 GAGCTGAGTTGCGGAGTGGA 62.160 60.000 0.00 0.00 38.13 4.02
639 679 1.739562 GAGCTGAGTTGCGGAGTGG 60.740 63.158 0.00 0.00 38.13 4.00
640 680 1.739562 GGAGCTGAGTTGCGGAGTG 60.740 63.158 0.00 0.00 38.13 3.51
641 681 1.910772 AGGAGCTGAGTTGCGGAGT 60.911 57.895 0.00 0.00 38.13 3.85
642 682 1.447489 CAGGAGCTGAGTTGCGGAG 60.447 63.158 0.00 0.00 38.13 4.63
643 683 2.659016 CAGGAGCTGAGTTGCGGA 59.341 61.111 0.00 0.00 38.13 5.54
644 684 2.435586 CCAGGAGCTGAGTTGCGG 60.436 66.667 0.00 0.00 38.13 5.69
645 685 1.447489 CTCCAGGAGCTGAGTTGCG 60.447 63.158 2.60 0.00 38.13 4.85
646 686 4.613929 CTCCAGGAGCTGAGTTGC 57.386 61.111 2.60 0.00 32.44 4.17
661 701 4.577246 CTACAGCTCCGCCCGCTC 62.577 72.222 0.00 0.00 35.07 5.03
663 703 4.452733 AACTACAGCTCCGCCCGC 62.453 66.667 0.00 0.00 0.00 6.13
664 704 2.509336 CAACTACAGCTCCGCCCG 60.509 66.667 0.00 0.00 0.00 6.13
665 705 2.125106 CCAACTACAGCTCCGCCC 60.125 66.667 0.00 0.00 0.00 6.13
666 706 0.321298 TTTCCAACTACAGCTCCGCC 60.321 55.000 0.00 0.00 0.00 6.13
667 707 1.666189 GATTTCCAACTACAGCTCCGC 59.334 52.381 0.00 0.00 0.00 5.54
668 708 2.932614 CTGATTTCCAACTACAGCTCCG 59.067 50.000 0.00 0.00 0.00 4.63
669 709 3.274288 CCTGATTTCCAACTACAGCTCC 58.726 50.000 0.00 0.00 0.00 4.70
670 710 3.055094 TCCCTGATTTCCAACTACAGCTC 60.055 47.826 0.00 0.00 0.00 4.09
671 711 2.912956 TCCCTGATTTCCAACTACAGCT 59.087 45.455 0.00 0.00 0.00 4.24
672 712 3.350219 TCCCTGATTTCCAACTACAGC 57.650 47.619 0.00 0.00 0.00 4.40
673 713 4.697352 CAGTTCCCTGATTTCCAACTACAG 59.303 45.833 0.00 0.00 41.50 2.74
674 714 4.651778 CAGTTCCCTGATTTCCAACTACA 58.348 43.478 0.00 0.00 41.50 2.74
675 715 3.440522 GCAGTTCCCTGATTTCCAACTAC 59.559 47.826 0.00 0.00 41.50 2.73
676 716 3.073798 TGCAGTTCCCTGATTTCCAACTA 59.926 43.478 0.00 0.00 41.50 2.24
677 717 2.158475 TGCAGTTCCCTGATTTCCAACT 60.158 45.455 0.00 0.00 41.50 3.16
678 718 2.238521 TGCAGTTCCCTGATTTCCAAC 58.761 47.619 0.00 0.00 41.50 3.77
679 719 2.673775 TGCAGTTCCCTGATTTCCAA 57.326 45.000 0.00 0.00 41.50 3.53
680 720 2.905415 ATGCAGTTCCCTGATTTCCA 57.095 45.000 0.00 0.00 41.50 3.53
681 721 4.498241 GAAAATGCAGTTCCCTGATTTCC 58.502 43.478 0.00 0.00 41.50 3.13
682 722 4.221482 AGGAAAATGCAGTTCCCTGATTTC 59.779 41.667 22.36 5.57 44.90 2.17
683 723 4.162651 AGGAAAATGCAGTTCCCTGATTT 58.837 39.130 22.36 6.00 44.90 2.17
684 724 3.766051 GAGGAAAATGCAGTTCCCTGATT 59.234 43.478 10.20 0.00 44.90 2.57
685 725 3.359950 GAGGAAAATGCAGTTCCCTGAT 58.640 45.455 10.20 0.27 44.90 2.90
686 726 2.795329 GAGGAAAATGCAGTTCCCTGA 58.205 47.619 10.20 0.00 44.90 3.86
687 727 1.470098 CGAGGAAAATGCAGTTCCCTG 59.530 52.381 10.20 7.87 44.90 4.45
688 728 1.826385 CGAGGAAAATGCAGTTCCCT 58.174 50.000 22.36 15.78 44.90 4.20
689 729 0.171231 GCGAGGAAAATGCAGTTCCC 59.829 55.000 22.36 11.03 44.90 3.97
690 730 1.168714 AGCGAGGAAAATGCAGTTCC 58.831 50.000 19.70 19.70 44.25 3.62
691 731 2.414691 GGAAGCGAGGAAAATGCAGTTC 60.415 50.000 0.00 1.80 0.00 3.01
692 732 1.541588 GGAAGCGAGGAAAATGCAGTT 59.458 47.619 0.00 0.00 0.00 3.16
693 733 1.168714 GGAAGCGAGGAAAATGCAGT 58.831 50.000 0.00 0.00 0.00 4.40
694 734 0.097674 CGGAAGCGAGGAAAATGCAG 59.902 55.000 0.00 0.00 0.00 4.41
695 735 0.321210 TCGGAAGCGAGGAAAATGCA 60.321 50.000 0.00 0.00 0.00 3.96
696 736 0.375106 CTCGGAAGCGAGGAAAATGC 59.625 55.000 0.00 0.00 32.81 3.56
697 737 2.010145 TCTCGGAAGCGAGGAAAATG 57.990 50.000 0.00 0.00 36.71 2.32
698 738 2.990066 ATCTCGGAAGCGAGGAAAAT 57.010 45.000 0.00 0.00 36.71 1.82
699 739 2.618053 GAATCTCGGAAGCGAGGAAAA 58.382 47.619 0.00 0.00 36.71 2.29
700 740 1.134788 GGAATCTCGGAAGCGAGGAAA 60.135 52.381 0.00 0.00 36.71 3.13
701 741 0.460311 GGAATCTCGGAAGCGAGGAA 59.540 55.000 0.00 0.00 36.71 3.36
702 742 0.395862 AGGAATCTCGGAAGCGAGGA 60.396 55.000 0.00 0.00 36.71 3.71
703 743 0.249238 CAGGAATCTCGGAAGCGAGG 60.249 60.000 0.00 0.00 36.71 4.63
704 744 0.249238 CCAGGAATCTCGGAAGCGAG 60.249 60.000 0.00 0.00 37.35 5.03
705 745 0.683179 TCCAGGAATCTCGGAAGCGA 60.683 55.000 0.00 0.00 0.00 4.93
706 746 0.249238 CTCCAGGAATCTCGGAAGCG 60.249 60.000 0.00 0.00 0.00 4.68
707 747 0.531753 GCTCCAGGAATCTCGGAAGC 60.532 60.000 0.00 0.00 0.00 3.86
708 748 0.249238 CGCTCCAGGAATCTCGGAAG 60.249 60.000 0.00 0.00 0.00 3.46
709 749 1.676678 CCGCTCCAGGAATCTCGGAA 61.677 60.000 11.67 0.00 39.23 4.30
710 750 2.127869 CCGCTCCAGGAATCTCGGA 61.128 63.158 11.67 0.00 39.23 4.55
711 751 2.419198 CCGCTCCAGGAATCTCGG 59.581 66.667 0.00 0.00 0.00 4.63
712 752 1.227089 CACCGCTCCAGGAATCTCG 60.227 63.158 0.00 0.00 34.73 4.04
713 753 1.144936 CCACCGCTCCAGGAATCTC 59.855 63.158 0.00 0.00 34.73 2.75
714 754 2.370445 CCCACCGCTCCAGGAATCT 61.370 63.158 0.00 0.00 34.73 2.40
715 755 2.190578 CCCACCGCTCCAGGAATC 59.809 66.667 0.00 0.00 34.73 2.52
716 756 1.789576 AAACCCACCGCTCCAGGAAT 61.790 55.000 0.00 0.00 34.73 3.01
717 757 2.406002 GAAACCCACCGCTCCAGGAA 62.406 60.000 0.00 0.00 34.73 3.36
718 758 2.852075 AAACCCACCGCTCCAGGA 60.852 61.111 0.00 0.00 34.73 3.86
719 759 2.359975 GAAACCCACCGCTCCAGG 60.360 66.667 0.00 0.00 37.30 4.45
720 760 2.359975 GGAAACCCACCGCTCCAG 60.360 66.667 0.00 0.00 0.00 3.86
721 761 4.323477 CGGAAACCCACCGCTCCA 62.323 66.667 0.00 0.00 43.74 3.86
727 767 1.602605 CCCTGTTCGGAAACCCACC 60.603 63.158 0.00 0.00 34.28 4.61
728 768 2.265904 GCCCTGTTCGGAAACCCAC 61.266 63.158 0.00 0.00 34.28 4.61
729 769 2.114411 GCCCTGTTCGGAAACCCA 59.886 61.111 0.00 0.00 34.28 4.51
730 770 1.844544 TAGGCCCTGTTCGGAAACCC 61.845 60.000 0.00 0.00 34.28 4.11
731 771 0.037160 TTAGGCCCTGTTCGGAAACC 59.963 55.000 0.00 0.00 34.28 3.27
732 772 1.538512 GTTTAGGCCCTGTTCGGAAAC 59.461 52.381 0.00 0.00 35.85 2.78
733 773 1.546099 GGTTTAGGCCCTGTTCGGAAA 60.546 52.381 0.00 0.00 33.16 3.13
734 774 0.037160 GGTTTAGGCCCTGTTCGGAA 59.963 55.000 0.00 0.00 33.16 4.30
735 775 0.838987 AGGTTTAGGCCCTGTTCGGA 60.839 55.000 0.00 0.00 33.16 4.55
736 776 0.906775 TAGGTTTAGGCCCTGTTCGG 59.093 55.000 0.00 0.00 33.35 4.30
737 777 2.773993 TTAGGTTTAGGCCCTGTTCG 57.226 50.000 0.00 0.00 33.35 3.95
738 778 4.659115 TCTTTTAGGTTTAGGCCCTGTTC 58.341 43.478 0.00 0.00 33.35 3.18
739 779 4.734843 TCTTTTAGGTTTAGGCCCTGTT 57.265 40.909 0.00 0.00 33.35 3.16
740 780 4.734843 TTCTTTTAGGTTTAGGCCCTGT 57.265 40.909 0.00 0.00 33.35 4.00
741 781 6.413783 TTTTTCTTTTAGGTTTAGGCCCTG 57.586 37.500 0.00 0.00 33.35 4.45
857 899 9.378551 AGATTCGTATAAACTGAAAGCATACAA 57.621 29.630 0.00 0.00 37.60 2.41
909 951 1.080772 CTGTGCTGTTACGGCGAGA 60.081 57.895 16.62 0.00 38.82 4.04
976 1018 1.029681 GGAAAGTTTGTCTGCGGGTT 58.970 50.000 0.00 0.00 0.00 4.11
977 1019 1.164041 CGGAAAGTTTGTCTGCGGGT 61.164 55.000 0.00 0.00 0.00 5.28
978 1020 1.574428 CGGAAAGTTTGTCTGCGGG 59.426 57.895 0.00 0.00 0.00 6.13
979 1021 1.574428 CCGGAAAGTTTGTCTGCGG 59.426 57.895 0.00 0.00 0.00 5.69
980 1022 1.082104 GCCGGAAAGTTTGTCTGCG 60.082 57.895 5.05 0.00 0.00 5.18
981 1023 1.285950 GGCCGGAAAGTTTGTCTGC 59.714 57.895 5.05 0.00 0.00 4.26
982 1024 1.068333 CATGGCCGGAAAGTTTGTCTG 60.068 52.381 5.05 0.00 0.00 3.51
983 1025 1.247567 CATGGCCGGAAAGTTTGTCT 58.752 50.000 5.05 0.00 0.00 3.41
988 1038 3.981308 CGACATGGCCGGAAAGTT 58.019 55.556 5.05 0.00 0.00 2.66
1163 1213 1.287442 AGAGAGATGCAGGAGTGAGGA 59.713 52.381 0.00 0.00 0.00 3.71
1166 1216 3.908476 ACATAGAGAGATGCAGGAGTGA 58.092 45.455 0.00 0.00 0.00 3.41
1279 1329 3.610040 TCAGGCATAATGTCGAACACT 57.390 42.857 0.00 0.00 0.00 3.55
1289 1339 2.283298 CGCTCACTGTTCAGGCATAAT 58.717 47.619 4.82 0.00 0.00 1.28
1314 1364 1.802960 GGATATCAGCGTTGCATCAGG 59.197 52.381 4.83 0.00 0.00 3.86
1336 1386 1.073923 AGACCGCAGAACCCAAAGAAT 59.926 47.619 0.00 0.00 0.00 2.40
1390 1441 2.348059 GGACACACAACAAAACGACGTA 59.652 45.455 0.00 0.00 0.00 3.57
1467 1518 1.672356 CCACAAGGAAGGCCAGACG 60.672 63.158 5.01 0.00 36.89 4.18
1469 1520 1.774217 ACCCACAAGGAAGGCCAGA 60.774 57.895 5.01 0.00 39.89 3.86
1475 1526 3.703001 ATCACTACACCCACAAGGAAG 57.297 47.619 0.00 0.00 39.89 3.46
1485 1536 7.553044 AGTTTAGCCTGAATAAATCACTACACC 59.447 37.037 0.00 0.00 33.47 4.16
1486 1537 8.494016 AGTTTAGCCTGAATAAATCACTACAC 57.506 34.615 0.00 0.00 33.47 2.90
1487 1538 9.515226 AAAGTTTAGCCTGAATAAATCACTACA 57.485 29.630 0.00 0.00 33.47 2.74
1517 1575 2.292267 ACCATTCAGAACATCGATGCC 58.708 47.619 25.11 16.60 0.00 4.40
1570 1629 9.455847 GCTCATAGTCATCCAATTCAAATTAAC 57.544 33.333 0.00 0.00 0.00 2.01
1790 1869 8.000709 TGTAGAAAATCATCATCTAGGGCAAAT 58.999 33.333 0.00 0.00 0.00 2.32
1858 1937 3.492102 AGCACAACATCAGTGTAAGGT 57.508 42.857 0.00 0.00 37.67 3.50
1898 1977 1.931172 GCAAGTTGAATCCATGCATGC 59.069 47.619 21.69 11.82 37.00 4.06
1932 2011 4.150897 AGGCTAAGCAATAAATCCGTCA 57.849 40.909 0.00 0.00 0.00 4.35
1943 2022 0.178992 ACTGGCACAAGGCTAAGCAA 60.179 50.000 7.82 0.00 44.01 3.91
2504 2584 4.836736 CCTCCAAGGATGAATTTGGCATAT 59.163 41.667 0.00 0.00 42.82 1.78
2737 2824 6.200665 GTGATAACTGATGAGAGCACAAGATC 59.799 42.308 0.00 0.00 0.00 2.75
2889 2997 3.213206 TCCAACAAGACTGCACAATCT 57.787 42.857 0.00 0.00 0.00 2.40
2956 3064 7.273320 TCTTCTAAACACTATAGCGTGCTAT 57.727 36.000 17.65 17.65 41.58 2.97
2963 3071 5.507650 CGGGACCTCTTCTAAACACTATAGC 60.508 48.000 0.00 0.00 0.00 2.97
2986 3094 0.389948 GACCAGTGTCCCTTAGCACG 60.390 60.000 0.00 0.00 40.26 5.34
2997 3105 4.574828 GTGTTCATGTGTTTAGACCAGTGT 59.425 41.667 0.00 0.00 0.00 3.55
3081 3189 0.610687 AGGATATGCCTCTTAGCGGC 59.389 55.000 6.25 6.25 46.97 6.53
3328 3436 5.851703 CGAAGATGCATGCTATCAATCTTTG 59.148 40.000 23.44 22.40 0.00 2.77
3352 3460 1.408969 TGTTTTCCAGCCCCTGAAAC 58.591 50.000 0.00 0.00 32.46 2.78
3824 4015 7.285401 GGATAAAGGCTTCTGTCAAATAATGGA 59.715 37.037 0.00 0.00 0.00 3.41
3825 4016 7.428826 GGATAAAGGCTTCTGTCAAATAATGG 58.571 38.462 0.00 0.00 0.00 3.16
3826 4017 7.428826 GGGATAAAGGCTTCTGTCAAATAATG 58.571 38.462 0.00 0.00 0.00 1.90
4067 4276 7.500559 ACTGATCAGCTTCCAGTTTAAATATCC 59.499 37.037 22.83 0.00 37.86 2.59
4181 4390 1.806542 GCCGGCATGTAAGATACCATG 59.193 52.381 24.80 0.00 0.00 3.66
4325 4534 9.533831 TGGCATTACTATATATGAGAGTCAAGA 57.466 33.333 0.00 0.00 30.41 3.02
4499 4708 2.932498 TGCGAATCTGAAAACATGTGC 58.068 42.857 0.00 0.00 0.00 4.57
4588 4798 2.436417 ACAATCACCACAGCCATGTAC 58.564 47.619 0.00 0.00 37.65 2.90
4628 4838 5.044558 AGATTTTCTCTCGGCTAAACGATC 58.955 41.667 0.00 0.00 42.62 3.69
4631 4841 4.389077 ACAAGATTTTCTCTCGGCTAAACG 59.611 41.667 0.00 0.00 31.03 3.60
4676 4891 4.631377 TCTCAAGGTTTCGAATGCATACTG 59.369 41.667 0.00 0.00 0.00 2.74
4701 4921 8.338259 CCATAGAATGATACAAAGTTCCGAAAG 58.662 37.037 0.00 0.00 0.00 2.62
4723 4943 8.523915 AGCTTTGACATCATAAACAATCCATA 57.476 30.769 0.00 0.00 0.00 2.74
4754 5144 3.658757 GCTGTCAGCCCAAAATACAAA 57.341 42.857 14.27 0.00 34.48 2.83
4799 5214 2.306341 ACTACATAGCAGCAGCACAG 57.694 50.000 3.17 0.00 45.49 3.66
4814 5229 7.253354 CGAAACAACAACGAGATGAGATACTAC 60.253 40.741 0.00 0.00 0.00 2.73
4815 5230 6.745907 CGAAACAACAACGAGATGAGATACTA 59.254 38.462 0.00 0.00 0.00 1.82
4816 5231 5.573282 CGAAACAACAACGAGATGAGATACT 59.427 40.000 0.00 0.00 0.00 2.12
4884 5299 8.314751 TCAAGGTAAACACAAAATTTTTGAGGA 58.685 29.630 24.73 7.43 0.00 3.71
4972 5390 2.128771 TGCTGAAGATAAAGCCCACC 57.871 50.000 0.00 0.00 38.71 4.61
5030 5481 2.270923 CTAGCAAGCATCGTTAGCACA 58.729 47.619 0.00 0.00 0.00 4.57
5080 5535 5.821470 GGATGGGATAATGCACTATCATCAG 59.179 44.000 16.38 0.00 31.01 2.90
5087 5542 5.163001 TGGAATTGGATGGGATAATGCACTA 60.163 40.000 0.00 0.00 0.00 2.74
5118 5573 2.977405 GCTGGAAACTAGCTGTGTTG 57.023 50.000 0.00 0.00 38.14 3.33
5192 5648 3.496160 GCGGAGATATTTTTCTGGGGCTA 60.496 47.826 0.00 0.00 0.00 3.93
5194 5650 1.609072 GCGGAGATATTTTTCTGGGGC 59.391 52.381 0.00 0.00 0.00 5.80
5213 5669 1.845809 CGGCTGGATATTTGCCTCGC 61.846 60.000 11.14 0.00 44.09 5.03
5215 5671 1.334869 CAACGGCTGGATATTTGCCTC 59.665 52.381 0.00 0.00 44.09 4.70
5216 5672 1.392589 CAACGGCTGGATATTTGCCT 58.607 50.000 0.00 0.00 44.09 4.75
5217 5673 3.944871 CAACGGCTGGATATTTGCC 57.055 52.632 0.00 0.00 42.94 4.52
5267 5723 3.200483 GGGTTTTATAGTGTACAGGGCG 58.800 50.000 0.00 0.00 0.00 6.13
5268 5724 3.548770 GGGGTTTTATAGTGTACAGGGC 58.451 50.000 0.00 0.00 0.00 5.19
5272 5728 4.225717 GTGGAGGGGGTTTTATAGTGTACA 59.774 45.833 0.00 0.00 0.00 2.90


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.